moo_sci_single.c

/*
 * This file is part of the MOONS Pipeline
 * Copyright (C) 2002-2016 European Southern Observatory
 *
 * This program is free software; you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation; either version 2 of the License, or
 * (at your option) any later version.
 *
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
 */
 
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
 
/*-----------------------------------------------------------------------------
                                   Includes
 -----------------------------------------------------------------------------*/
#include <math.h>
#include <cpl.h>
#include "moo_pfits.h"
#include "moo_sci_single.h"
#include "moo_fits.h"
#include "moo_qc.h"
#include "moo_badpix.h"
#include "moo_utils.h"
/*----------------------------------------------------------------------------*/
/*----------------------------------------------------------------------------*/
 
/*-----------------------------------------------------------------------------
                              Function codes
 -----------------------------------------------------------------------------*/
 
/*----------------------------------------------------------------------------*/
/*----------------------------------------------------------------------------*/
moo_sci_single *
moo_sci_single_new(moo_detector_type type)
{
    moo_sci_single *res = cpl_calloc(1, sizeof(moo_sci_single));
    res->badpix_mask = MOO_BADPIX_GOOD;
    res->type = type;
    const char *extname = moo_detector_get_name(type);
    res->extname = extname;
    res->header = cpl_propertylist_new();
    return res;
}
 
/*----------------------------------------------------------------------------*/
/*----------------------------------------------------------------------------*/
 
void
moo_sci_single_delete(moo_sci_single *self)
{
    if (self != NULL) {
        if (self->header != NULL) {
            cpl_propertylist_delete(self->header);
            self->header = NULL;
        }
        if (self->image != NULL) {
            hdrl_image_delete(self->image);
        }
        if (self->qual != NULL) {
            cpl_image_delete(self->qual);
        }
        if (self->sky != NULL) {
            cpl_image_delete(self->sky);
        }
        cpl_free(self);
    }
}
 
 
/*----------------------------------------------------------------------------*/
/*----------------------------------------------------------------------------*/
void
moo_sci_single_save(moo_sci_single *self,
                    const char *filename,
                    moo_detector_type type)
{
    const char *extname = moo_detector_get_name(type);
 
    if (self != NULL && self->image != NULL) {
        moo_fits_write_extension_image(hdrl_image_get_image(self->image),
                                       filename, NULL, extname,
                                       MOO_SCI_SINGLE_DATA_TYPE, self->header);
 
        cpl_propertylist *err_header = cpl_propertylist_new();
        moo_pfits_append_hduclass_error(err_header, type, -1, self->header);
 
        moo_fits_write_extension_image(hdrl_image_get_error(self->image),
                                       filename, MOO_SCI_SINGLE_ERR, extname,
                                       MOO_SCI_SINGLE_ERR_TYPE, err_header);
        cpl_propertylist_delete(err_header);
        cpl_propertylist *qual_header = cpl_propertylist_new();
        moo_pfits_append_hduclass_quality(qual_header, type, -1, self->header,
                                          self->badpix_mask);
        moo_fits_write_extension_image(self->qual, filename,
                                       MOO_SCI_SINGLE_QUAL, extname,
                                       MOO_SCI_SINGLE_QUAL_TYPE, qual_header);
        cpl_propertylist_delete(qual_header);
    }
    else {
        cpl_propertylist *h = cpl_propertylist_new();
        cpl_propertylist_append_string(h, MOO_PFITS_EXTNAME, extname);
        cpl_propertylist_save(h, filename, CPL_IO_EXTEND);
        cpl_propertylist_delete(h);
 
        moo_fits_write_extension_image(NULL, filename, MOO_SCI_SINGLE_ERR,
                                       extname, MOO_SCI_SINGLE_ERR_TYPE, NULL);
        moo_fits_write_extension_image(NULL, filename, MOO_SCI_SINGLE_QUAL,
                                       extname, MOO_SCI_SINGLE_QUAL_TYPE, NULL);
    }
 
    if (self != NULL && self->sky != NULL) {
        cpl_propertylist *sky_header = cpl_propertylist_new();
        cpl_propertylist_copy_property(sky_header, self->header,
                                       MOO_PFITS_BUNIT);
        cpl_propertylist_copy_property(sky_header, self->header,
                                       MOO_PFITS_CRPIX1);
        cpl_propertylist_copy_property(sky_header, self->header,
                                       MOO_PFITS_CRVAL1);
        cpl_propertylist_copy_property(sky_header, self->header,
                                       MOO_PFITS_CD1_1);
        cpl_propertylist_copy_property(sky_header, self->header,
                                       MOO_PFITS_CTYPE1);
        cpl_propertylist_copy_property(sky_header, self->header,
                                       MOO_PFITS_CUNIT1);
        /*
    cpl_propertylist_append_double(res->header,MOO_PFITS_CRPIX2,MOO_EXT_SINGLE_CRPIX2);
    cpl_propertylist_append_double(res->header,MOO_PFITS_CRVAL2,MOO_EXT_SINGLE_CRVAL2);
    cpl_propertylist_append_double(res->header,MOO_PFITS_CDELT2,MOO_EXT_SINGLE_CDELT2);
    cpl_propertylist_append_string(res->header,MOO_PFITS_CTYPE2,MOO_EXT_SINGLE_CTYPE2);
*/
        moo_fits_write_extension_image(self->sky, filename, MOO_SCI_SINGLE_SKY,
                                       extname, CPL_TYPE_FLOAT, sky_header);
        cpl_propertylist_delete(sky_header);
    }
    else {
        moo_fits_write_extension_image(NULL, filename, MOO_SCI_SINGLE_SKY,
                                       extname, MOO_SCI_SINGLE_ERR_TYPE, NULL);
    }
}
 
/*----------------------------------------------------------------------------*/
/*----------------------------------------------------------------------------*/
moo_sci_single *
moo_sci_single_create(const char *filename, moo_detector_type type)
{
    cpl_ensure(filename != NULL, CPL_ERROR_NULL_INPUT, NULL);
 
    moo_sci_single *single = NULL;
    cpl_propertylist *header = NULL;
 
    const char *extname = moo_detector_get_name(type);
 
    header = moo_fits_load_extension_header(filename, NULL, extname);
    if (header != NULL) {
        int naxis = moo_pfits_get_naxis(header);
        if (naxis > 0) {
            single = moo_sci_single_new(type);
            single->filename = filename;
            cpl_propertylist_append(single->header, header);
        }
        cpl_propertylist_delete(header);
    }
    return single;
}
 
/*----------------------------------------------------------------------------*/
/*----------------------------------------------------------------------------*/
cpl_error_code
moo_sci_single_load(moo_sci_single *self, unsigned int level)
{
    if (self != NULL) {
        if ((self->filename != NULL) && (self->extname != NULL)) {
            if (self->header == NULL) {
                cpl_size extnum =
                    cpl_fits_find_extension(self->filename, self->extname);
                if (extnum > 0) {
                    self->header =
                        cpl_propertylist_load(self->filename, extnum);
                }
            }
            if (self->qual == NULL) {
                self->qual =
                    moo_fits_load_extension_image(self->filename,
                                                  MOO_SCI_SINGLE_QUAL,
                                                  self->extname, CPL_TYPE_INT);
            }
            if (self->image == NULL) {
                cpl_image *data = NULL;
                cpl_image *err = NULL;
 
                data = moo_fits_load_extension_image(self->filename, NULL,
                                                     self->extname,
                                                     CPL_TYPE_DOUBLE);
                err = moo_fits_load_extension_image(self->filename,
                                                    MOO_SCI_SINGLE_ERR,
                                                    self->extname,
                                                    CPL_TYPE_DOUBLE);
 
                if (data != NULL && err != NULL) {
                    self->image = hdrl_image_create(data, err);
                    cpl_image_delete(data);
                    cpl_image_delete(err);
                }
            }
            self->sky = moo_sci_single_get_sky(self);
        }
 
        cpl_mask *mask = hdrl_image_get_mask(self->image);
        moo_badpix_to_mask(self->qual, mask, level);
    }
    return CPL_ERROR_NONE;
}
 
/*----------------------------------------------------------------------------*/
/*----------------------------------------------------------------------------*/
hdrl_image *
moo_sci_single_get_image(moo_sci_single *self)
{
    cpl_ensure(self != NULL, CPL_ERROR_NULL_INPUT, NULL);
 
    return self->image;
}
 
/*----------------------------------------------------------------------------*/
/*----------------------------------------------------------------------------*/
cpl_propertylist *
moo_sci_single_get_header(moo_sci_single *self)
{
    cpl_ensure(self != NULL, CPL_ERROR_NULL_INPUT, NULL);
 
    if (self->header == NULL && self->filename != NULL &&
        self->extname != NULL) {
        self->header =
            moo_fits_load_extension_header(self->filename, NULL, self->extname);
        if (self->header == NULL) {
            self->header = cpl_propertylist_new();
        }
    }
    return self->header;
}
 
/*----------------------------------------------------------------------------*/
/*----------------------------------------------------------------------------*/
cpl_image *
moo_sci_single_get_sky(moo_sci_single *self)
{
    cpl_ensure(self != NULL, CPL_ERROR_NULL_INPUT, NULL);
 
    if (self->sky == NULL && self->filename != NULL && self->extname != NULL) {
        self->sky =
            moo_fits_load_extension_image(self->filename, MOO_SCI_SINGLE_SKY,
                                          self->extname, CPL_TYPE_DOUBLE);
    }
    return self->sky;
}
 
/*----------------------------------------------------------------------------*/
/*----------------------------------------------------------------------------*/
cpl_image *
moo_sci_single_get_qual(moo_sci_single *self)
{
    cpl_ensure(self != NULL, CPL_ERROR_NULL_INPUT, NULL);
 
    if (self->qual == NULL) {
        cpl_ensure(self->filename != NULL, CPL_ERROR_NULL_INPUT, NULL);
        cpl_ensure(self->extname != NULL, CPL_ERROR_NULL_INPUT, NULL);
        self->qual =
            moo_fits_load_extension_image(self->filename, MOO_SCI_SINGLE_QUAL,
                                          self->extname,
                                          MOO_SCI_SINGLE_QUAL_TYPE);
    }
    return self->qual;
}
 
/*----------------------------------------------------------------------------*/
/*----------------------------------------------------------------------------*/
double
moo_sci_single_compute_snr(moo_sci_single *self,
                           int targ_idx,
                           moo_sky_lines_list *skylines)
{
    double snr = NAN;
 
    double *zwmin = NULL;
    double *zwmax = NULL;
    cpl_array *sel = NULL;
    cpl_vector *data = NULL;
    hdrl_image *fimg = NULL;
    cpl_vector *row = NULL;
 
    cpl_ensure(self != NULL, CPL_ERROR_NULL_INPUT, 0.0);
    cpl_errorstate prev_state = cpl_errorstate_get();
 
    hdrl_image *himg = moo_sci_single_get_image(self);
    cpl_propertylist *header = moo_sci_single_get_header(self);
    int nx = hdrl_image_get_size_x(himg);
    double crpix1 = moo_pfits_get_crpix1(header);
    double cd1_1 = moo_pfits_get_cd1_1(header);
    double crval1 = moo_pfits_get_crval1(header);
    double wmin = (0.5 - crpix1) * cd1_1 + crval1;
    double wmax = (nx + 0.5 - crpix1) * cd1_1 + crval1;
 
 
    moo_try_check(moo_sky_lines_list_get_free_zones(skylines, wmin, wmax,
                                                    &zwmin, &zwmax, &sel),
                  " ");
    int size = cpl_array_get_size(sel);
 
    for (int i = 0; i < size; i++) {
        int idx = cpl_array_get_cplsize(sel, i, NULL);
        double cmin = zwmin[idx];
        double cmax = zwmax[idx];
        int start = (cmin - crval1) / cd1_1 + crpix1;
        int stop = (cmax - crval1) / cd1_1 + crpix1;
        fimg = hdrl_image_extract(himg, start, targ_idx, stop, targ_idx);
        hdrl_image_reject_value(fimg, CPL_VALUE_NAN);
        cpl_image *img = hdrl_image_get_image(fimg);
        cpl_image *error = hdrl_image_get_error(fimg);
        cpl_image_reject_value(error, CPL_VALUE_NAN | CPL_VALUE_ZERO);
        cpl_image_divide(img, error);
        row = cpl_vector_new_from_image_row(img, 1);
        if (data == NULL) {
            data = cpl_vector_duplicate(row);
        }
        else {
            int vsize = cpl_vector_get_size(data);
            int row_size = cpl_vector_get_size(row);
            cpl_vector_set_size(data, vsize + row_size);
            for (int j = 0; j < row_size; j++) {
                double v = cpl_vector_get(row, j);
                cpl_vector_set(data, j + vsize, v);
            }
        }
        cpl_vector_delete(row);
        hdrl_image_delete(fimg);
        fimg = NULL;
        row = NULL;
    }
    snr = cpl_vector_get_median(data);
 
moo_try_cleanup:
    if (!cpl_errorstate_is_equal(prev_state)) {
        cpl_vector_delete(row);
        hdrl_image_delete(fimg);
        snr = NAN;
        cpl_msg_error(__func__, "Can't compute snr for target %d", targ_idx);
        cpl_errorstate_set(prev_state);
    }
    cpl_vector_delete(data);
    cpl_array_delete(sel);
    return snr;
}
/*----------------------------------------------------------------------------*/